Soy products have become ubiquitous food additives due to their many health-promoting properties. Sadly, not everyone's health has been improved: soy allergies are on the rise. From 1998 to 1999, there was a 50% increase in the number of people reporting problems with soy.
According to a survey of pediatricians in the U.S., 1.1% of all infants are allergic to soy (as a comparison, 3.4% are allergic to cow's milk). An international survey of otherwise-healthy babies indicated that 0.5% of all infants are allergic to soy. In Sweden, there were four documented deaths due to anaphylactic shock from soy consumption during the mid-90s.
I discovered I was allergic to soy products right after I developed a real taste for miso soup. In my case, the allergy is fairly mild overall, but I get severe sinus headaches and congestion as a result and my overall allergies get worse. My symptoms were subtle enough that it took me about a year to figure out that my frequent "colds" weren't due to Columbus being Plague Central.
Soy proteins are in many types of less-refined soybean oil, and can consequently be in foods like margarine. Unfortunately, you can't tell which oils have been sufficiently purified. If your allergy is mild (as mine is) you probably don't have to worry about the protein content in oil. But you should watch out for whole soybean foods and foods (particularly health-food snacks like Balance Bars and Powerbars) that contain refined or isolated soy proteins as additives. Soy lecithin is in a whole lot of foods.
The bad part about food allergies is that for some folks they tend to get worse over time. And you can suddenly get sensitized to a protein and develop a whole new allergy. People who as children or infants were allergic to cow's milk have an increased risk of developing a soy allergy later on in life (however, overall soy is less likely to provoke an allergy than milk is). Thus, if you are the parent of a milk-allergic child and you give him or her soy products as a dairy substitute, you should watch the child carefully for signs of allergy.
These allergies often have a genetic component. So, if you have a soy allergy, particularly a severe one, you probably shouldn't give soy products to your very young children. Children under the age of 3 months are particularly vulnerable to developing soy allergies; the risk goes down dramatically after they're a year old. Some children who have trouble with soy when they're infants can process it when they're 5 or older.
The main proteins in soy that seem to cause problems are two heat-stable (i.e., they stay intact after cooking) globulins named beta-conglycin and glycinin. These two proteins comprise 90% of the total proteins in soybeans. However, researchers have identified nine other proteins in soybeans that have provoked antibody responses in lab tests; furthermore, these proteins may be broken down during digestion into other proteins that could act as antigens and cause problems in sensitive people.
References: http://www.emedicine.com/ped/topic2128.htm and http://www.tldp.com/issue/11_00/joysoy.htm